NCBO Wiki - User contributions [en]

Visualizing Concepts and Mappings

2015-11-03T18:59:26Z

The CHISEL Group:

With BioPortal, you can visualize ontology concepts and their mappings with other ontologies. To view a larger version of any of the images in this document, click the desired image.
<h2>How BioPortal displays concepts and mappings</h2>
BioPortal displays ontologies as a graph: ontology concepts are represented by nodes in the graph, and the relationships among concepts are displayed as edges between the nodes. By default, the most basic directional relationships (parent/child relationships) are identified by a solid navy-blue line with an arrow pointing to the child concept. Mappings are identified by a solid light-grey line. However, depending on the construction of your ontology, BioPortal can [[#Adjusting the display of edges between concepts|display other types of relationships]]. The concept that you use to start a visualization is highlighted with a black border.

{| style="width:75%; height:200px" border="0" align="center"
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|align="center"|[[Image:Nodes.png|200px]]||align="center"|[[Image:NodesMappings.png|385px]]
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|align="center"|''Child concept (Respiratory System) with a solid arc and arrow pointing from its parent concepts (Organ System and Anatomic Structure, System, or Substance).''
|align="center"|''The same parent/child relationship including a mapping (Respiratory System) from another ontology. The mapping has also been expanded to show a parent concept (Body System).''
|}
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You can visualize any ontology by opening the ontology’s Summary page and clicking '''Classes'''. This displays details about the top-level concept in the ontology. From here, you can [[#Viewing concepts and mappings|view concepts and mappings]].

[[Image:DisplayClasses.png|500px]]

You can also [[#Viewing an overview of the mappings to an ontology|visualize a summary of ontologies mapped to a specified ontology]] by clicking the '''Mappings''' tab from the BioPortal Home page.

<h2>Viewing concepts and mappings</h2>
{| border="0"
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|To get started, open the '''Details''' page for a concept, and click the '''Visualization''' tab. This opens the Visualization panel and displays the ''Path to Root'' which contains the concept and all parent concepts, up to and including the root concept.

You can also display the ''Term Neighbourhood'' which contains the immediate parent and children of the current concept, or the ''Mappings Neighbourhood'' which contains the mappings for the current concept. To do this, click the drop-down arrow in the top-left portion of the Visualization panel, and select '''Term Neighbourhood''' or '''Mappings Neighbourhood'''. From here, you can drag concepts around the screen to optimize viewing. You can also display mappings, other concepts, and adjust the style of visualization used.
| [[Image:DisplayVisualization.png|400px]]
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|When visualizing an ontology, you can display a menu of tools that allow you to work with and customize your visualization. To open the tools menu, click '''Menu''' in the upper-right corner of your visualization.
* '''Layout''': This tool allows you to control the [[#Layouts|layout of the visualization]].
* '''Node Utilities''': This tool allows you to [[#Searching for concepts|search for a concept in your visualization]] or [[#Adding a concept to a visualization using its unique ID|add a concept by its BioPortal identifier]].
* '''Sharing''': This option allows you to export a visualization for [[#Sharing and saving visualizations|sharing with others]], or import a visualization that someone sent you.
* '''Edge Types Displayed''': This option [[#Adjusting the display of edges between concepts|displays a list of all the different concept relationships]] in your visualization. It also allows you to change the colors of the lines used for each relationship, and dim (grey out) or remove the concepts associated with certain types of relationships.
* '''Ontologies and Concepts Displayed''': This option [[#Controlling the display of concepts and ontologies|displays a list of all the concepts and ontologies]] displayed in your visualization. It also allows you to dim (grey out) or remove the concepts or ontologies displayed.
* '''Node Expansions Displayed''': This option [[#Working with node expansions|displays a list of Expansion Sets]]—groupings of concepts that you added to the visualization at a specific moment in time. It allows you to dim (grey out) or remove the concepts or ontologies displayed without having to select one concept at a time.
* '''Minimap''': This displays a small overview of your visualization and is handy when you are working with many concepts, especially if they scroll off the screen. You can drag the grey box to focus your visualization on a particular area of interest.
| [[Image:BioMixerOverview.png|650px]]
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<h3>Undoing and redoing actions</h3>
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|BioPortal provides a few options for backing out of or reapplying a change to a visualization. To move back or forward one step, click the large back or forward arrow in the top-left portion of the Visualization panel. To go back or forward several steps, click the small arrow to display a drop-down list of previously performed or previously undone actions.
Please note that the undo and redo tools do not work with the check box-style filters in the tools menu. However, undo/redo will work if you have removed a concept, ontology, or node expansion from the tools menu. In addition, the tools do not work with color changes, nor with layout changes that are not followed by the addition or removal of a node---this way, moving a single node repeatedly won't make a long and useless undo list.
| [[Image:UndoRedo.png|250px]]
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<h3>Viewing information about a concept or relationship</h3>
You can click a concept to display detailed information about it and the ontology it resides in.

[[Image:ClickConcept.png|450px]]

You can also hover over a line to [[#Adjusting the display of edges between concepts|determine the type of relationship]] between two concepts.

[[Image:HoverOverEdge.png|450px]]

<h2>Searching for concepts</h2>
When working with a visualization, you can search for a concept that is displayed in the graph. To do this, open the '''Node Utilities''' section of the tools menu and paste or type the characters or full name you’d like to locate in the visualization. Click the '''Locate Node''' button. BioPortal briefly highlights the matching concepts using an animated blue circle.

[[Image:LocateNode.png|450px]]

<h2>Displaying other concepts</h2>
{| border="0"
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|Once you have visualized a concept, you can expand the visualization to include the child or mapped concepts from any item. To do this, click the light-blue arrow beneath the desired concept and then select:
* '''Expand Concepts''': This option displays the children of the concept, if applicable.
* '''Expand Mappings''': This option displays any mappings related to the concept, if applicable.
* '''Refocus Node''': This will regenerate the visualization using the selected concept as the focus. All other nodes will be removed.
* '''Dim Node''': This option greys out the concept. For more information, see [[#Removing a concept from a visualization|Removing a mapping or concept from a visualization]].

This makes it possible to visualize multiple ontologies at once and see the relationships between them. To make it easier to see relationships, BioPortal [[#Controlling the display of concepts and ontologies|uses colors to identify ontologies]]. However, depending on how many ontologies you are working with, some colors may be duplicated.
Each time you expand a concept or display mappings, BioPortal treats this as an Expansion Set. The tools menu contains options for [[#Working with node expansions|working with Expansion Sets]] so that you can easily reduce or increase the complexity of a visualization without having to manually adjust the display of multiple nodes.
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<h3>Adding a concept to a visualization using its unique ID</h3>
Every concept stored in the system has a unique ID associated with it. This ID is a uniform resource identifier (URI) that looks like a Website address. You can find this ID by viewing the details associated with any concept.

[[Image:ConceptURI.png |450px]]

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|When working with a visualization, you can add a desired concept to the graph by entering that concept’s ID (URI). This also allows you to begin searching for potential connections between distant nodes within the same or different ontologies. To do this, open the '''Node Utilities''' section of the tools menu and paste or type the URI of the concept you’d like to add to the visualization. Click the '''Add Concept Using URI''' button.
| [[Image:AddConceptByURI.png|250px]]
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<h3>Removing a concept from a visualization</h3>
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|If a concept is no longer of interest to you, you can grey out the concept (or all concepts in a specific ontology) or entirely remove it from the visualization. There are two ways to do this. If you want to grey out a single concept, you can click the light-blue arrow beneath any concept in a visualization and select '''Dim Node'''. If you want to grey out multiple concepts, remove one or more concepts, or if you want to redisplay a greyed out concept, open the [[#Controlling the display of concepts and ontologies|'''Ontologies and Concepts Displayed''']] section of the tools menu.
| [[Image:DisplayDropDownMenu.png|150px]]
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<h2>Changing how concepts are displayed</h2>
When visualizing ontology information, you can adjust how concepts are displayed from the tools menu. To open the tools menu, click '''Menu''' in the upper-right corner of your visualization.

<h3>Layouts</h3>
You can adjust the style of graph used to optimize the display of your visualization and to make it easier to view related information. The Layouts portion of the tools menu displays six different layouts:
* '''Center Layout''': This layout centers the concept that you used to start the visualization and positions all other concepts around it.
* '''Circle Layout''': This layout displays the concepts in a circle.
* '''Vertical Layout''': This layout displays the concepts and child/parent relationships organized vertically.
* '''Horizontal Layout''': This layout displays the concepts and child/parent relationships organized horizontally.
* '''Force-Directed Layout''': This layout positions the concepts so that all the edges are of more or less equal length and with as few crossing edges as possible. Use the Force-Directed Layout when working with clusters of data to optimize the display of related groups of information.
* '''Radial Layout''': This layout displays the concepts outwards radially according to their hierarchy in the tree.

<h3>Adjusting the display of edges between concepts</h3>
{| border="0"
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|The relationships among concepts are displayed as edges between nodes. By default, the most basic directional relationships (parent/child relationships) are identified by a solid navy-blue line with an arrow pointing to the child concept. Mappings are identified by a solid light-grey line. However, BioPortal will display any other types of relationships defined by the ontology. If desired, you can change the colors used by the various types of edges. You can also temporarily filter (remove) certain edge types from your visualization: this may be useful when working with a complex visualization.
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|To change the color of an edge type, open the '''Edge Types Displayed''' section of the tools menu. This section displays all the different edge types used in your visualization. Click the line associated with the desired edge and a color pallet will open where you can select a new color. Once you have selected a color, click the Choose button at the bottom of the palette and the color will be applied to the visualization.
To filter an edge type in your visualization, open the '''Edge Types Displayed''' section of the tools menu and clear the desired check box. This will remove all lines associated with that type of edge from the visualization. To add them back in, reselect the check box.
| [[Image:ChooseColor.png|150px]]
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<h3>Controlling the display of concepts and ontologies</h3>
{| border="0"
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|You can grey out multiple concepts or remove one or more concepts from a visualization. To do this, open the '''Ontologies and Concepts Displayed''' section of the tools menu. This section displays all the ontologies used in your visualization: each concept displayed is listed under the name of its ontology. When working with large numbers of concepts, use the '''Plus''' (+) and '''Minus''' (-) icons to expand or condense each ontology.

To grey out an item, clear the check box. That item will be greyed out in your visualization. To redisplay a greyed out concept or ontology, reselect the check box.
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|align="center"|[[Image:ConceptsDisplayedAll.png|500px]]||align="center"|[[Image:ConceptsGreyedOut.png|500px]]
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|align="center"|''All concepts displayed.''
|align="center"|''All concepts under SNOMEDCT greyed out.''
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If you would like to remove the item fully, after clearing the check box, click the '''X''' in the upper-right corner of the Ontologies and Concepts Displayed section of the tools menu. This removes the concepts from the visualization—you can use the Undo tool to revert this change.

<h3>Working with node expansions</h3>
{| border="0"
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|Each time you expand a concept or display mappings, BioPortal treats this as an Expansion Set. The tools menu contains filtering options for working with Expansion Sets so that you can easily reduce or increase the complexity of a visualization without having to manually adjust the display of multiple nodes.

To view the Expansion Sets in your visualization, open the '''Node Expansions Displayed''' section of the tools menu. This section displays all the Expansion Sets generated as you work with your visualization. Under each set is a list of all the concepts affected by that change: use the Plus (+) and Minus (-) icons to expand or condense each set. To grey out a concept or an entire Expansion Set, clear the desired check box. To redisplay a greyed out item, reselect the check box.
| [[Image:ExpansionSets.png|250px]]
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<h2>Sharing and saving visualizations</h2>
BioPortal provides two options for sharing or saving a fully-formed visualization: you can send a digital image (screenshot) to anyone with a computer, or you can export a visualization to another BioPortal user.
To take a screenshot, click the '''Screenshot''' button in the upper-right corner of your visualization. You will be presented with options to save the image to your computer.
To export a visualization to another BioPortal user, open the '''Sharing''' section of the tools menu. Click the '''Export''' button and copy the specially-formatted text. You can then paste the text into an email.
To import a visualization, open the '''Sharing''' section of the tools menu. Click the Import button, paste the specially-formatted text and click '''Apply'''. The visualization will load in BioPortal where you can view it as is or start manipulating it.

<h2>Viewing an overview of the mappings to an ontology</h2>
You can visualize a summary of ontologies mapped to a specified ontology by clicking the '''Mappings''' tab from the BioPortal Home page.

[[Image:DisplayMappings.png|500px]]

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|Ontology nodes are displayed as two circles, with the inner circle representing the number of concepts mapped to the central ontology, and the outer circle representing the total number of concepts. You can use the slider to control the display of mapped ontologies based on the total number of mapped nodes. You can hover over a node to display key information about the ontology, including the percentage of the ontology that is mapped with the specified ontology on the Mappings page.
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BioPortal Help

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The CHISEL Group:

== User Interface ==
=== Home Page ===

BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to
* [[#Browse Tab|browse the library]] of ontologies
* [[#Search Tab|search for a term]] across multiple ontologies
* [[#Mappings Tab|browse mappings]] between terms in different ontologies
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus
* [[#Annotator Tab|annotate text]] with terms from ontologies
* [[#Resource Index Tab|search biomedical resources]] for a term
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources

All information available through the BioPortal Web site is also available through the NCBO Web service REST API. Please see [http://www.bioontology.org/wiki/index.php/NCBO_REST_services REST API documentation] for more information.

=== Browse Tab ===

Browse our library of Biomedical ontologies and submit your own ontology. This page displays some summary information about each ontology. More detailed summary information is available on the ontology summary page for each ontology. You can reach this page by clicking on the ontology name link.

To '''find a particular ontology quickly''', begin typing the ontology name or abbreviation in the “Filter by Text” field. You can also narrow the list of ontologies shown by selecting a specific “category” (a domain) or a “group” to which the ontology belongs. To '''submit an ontology''' press the “Submit New Ontology” button. You must be logged in to BioPortal to submit an ontology. You can subscribe to '''receive RSS updates''' when any ontology in the system changes by clicking the subscribe link. You can subscribe to updates for a particular ontology from the summary page for that ontology. To go to the summary page click on the ontology name link.

Some submitters want to control who can browse the terms in their ontology. These ontologies are marked with visibility “Private” or “Licensed”. To browse the terms in these ontologies you must be both
* logged in to BioPortal
* granted access to the ontology
For '''private ontologies''', the ontology submitter directly controls access to the ontology. Please contact the submitter to gain access to a private ontology. Contact information for the ontology is available on the ontology summary page. For '''licensed ontologies''', the submitter indirectly controls access to the ontology. When you attempt to access a licensed ontology, the system will prompt you to enter the license information required by the submitter. When you have entered the required information, the system will allow you to access the ontology. In addition, there are '''"summary only" ontologies'''. The terms for these ontologies are not available in BioPortal at all. Please contact the ontology submitter for more information about these ontologies.

To '''access ontologies programmatically''', see our [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Services_to_access_ontologies_and_ontology_versions Ontology REST API documentation].

=== Search Tab ===

Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text.

To '''find a term in any ontology''' enter the full or partial name the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link.

Note that, for performance reasons, only the top 100 matches are returned. Usually this number is sufficient to cover matches in all names, ids, and synonyms.

Some boolean search capability is available. Prefixing a term with "-" means NOT for that term. Thus "heart -attack" will search for terms with "heart" but not "attack" in the name. An OR capability is also available using parentheses. Thus "(heart attack)" means to find terms with either "heart" or "attack" in the name.

To '''search programmatically''' see our [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services Search REST API documentation].

=== Mappings Tab ===

Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).

To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.

To '''access mappings programmatically''', please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mappings REST API documentation].

=== Recommender Tab ===

The Recommender accepts text or a set of keywords describing a domain of interest; it then suggests appropriate ontologies to use if you want to identify terms in similar text.

The '''ontology ranking algorithm''' is described in the paper [http://www.ncbi.nlm.nih.gov/pubmed/20626921 Jonquet et al J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1].

To '''retrieve ontology recommendations programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service Ontology Recommender REST API documentation].

=== Annotator Tab ===

To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids.

In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.

To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].

Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]

=== Resource Index Tab ===

The resource index is a pre-calculated set of annotations of selected biomedical resources. We have used the Annotator web service to annotate these resources with all terms in all ontologies in BioPortal. To retrieve records annotated with a specific ontology term, select the term in the search box and press the "Search" button.

To '''access annotations for resources programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Resource_Index_REST_Web_Service_User_Guide Resource Index REST API documentation].

Further information on ontology-based search and mining of biomedical resources is available in [http://www.ncbi.nlm.nih.gov/pubmed/21918645 Jonquet et al Web Semant. 2011 Sep 1;9(3):316-324], [http://www.ncbi.nlm.nih.gov/pubmed/21550421 LePendu et al J Biomed Inform. 2011 Dec;44 Suppl 1:S31-8] and [http://www.ncbi.nlm.nih.gov/pubmed/22494789 Liu et al J Am Med Inform Assoc. 2012 Apr 11]

If you know of a publicly available biomedical resource that you would like to see in the Resource Index please send a request to include it to support@bioontology.org.

=== Projects Tab ===

This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create New Project" button. You must be logged in to BioPortal to create a new project.

== Common Tasks ==

=== Submitting an ontology ===
Go to the "Browse" page and press the "Submit Ontology" button near the top of the page.

=== Viewing and editing mappings ===
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.

To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.

=== Viewing and editing notes ===
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.

To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.

=== Viewing and editing reviews ===
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.

=== Visualizing concepts and mappings ===
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].

== Programing with the BioPortal API ==
Documentation about how to use the BioPortal REST API to access information is available here:

http://www.bioontology.org/wiki/index.php/NCBO_REST_services

== Glossary ==
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought.
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies.
; deprecated term: synonym for "obsolete term" in some ontologies.
; group: a collection of ontologies that are typically associated with some outside group or organization.
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms).
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.
; <span id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.
; term mappings: Set of mappings for a given term to terms other ontologies.
; term resources: Set of resources that contain annotations for a given term.

== How to cite NCBO and BioPortal ==
=== BioPortal ===
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.

=== NCBO ===
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.

=== SPARQL Endpoint ===
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.

Visualizing Concepts and Mappings

2012-11-22T23:23:02Z

The CHISEL Group: How to use BioPortal's concept and mapping visualization tools

With BioPortal, you can visualize ontology concepts and their mappings with other ontologies. The following information is available on this page:
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<h2>How BioPortal displays concepts and mappings</h2>
BioPortal displays individual ontology concepts and mappings as nodes. Lines are used to indicate the relationships among concepts and mappings. Directional relationships (parent/child relationships) are identified by a solid line with an arrow pointing to the parent concept. Mappings are identified by a dotted line.

{| style="width:75%; height:200px" border="0"
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|align="center"|[[Image:BioMixerEmbedNodes.png]]||align="center"|[[Image:BioMixerEmbedRelationships.png]]
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|align="center"|''Child concept (Respiratory System Agent) with a solid arc and arrow pointing to its parent concept (Therapeutic Categories).''
|align="center"|''The same parent/child relationship including a mapping (Respiratory drugs) from the child concept.''
|}
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<h2>Viewing concepts and mappings</h2>
To get started, open the '''Term Details''' page for a concept, and click the '''Visualization''' tab.

[[Image:BioMixerEmbedTermDetailsVisualizationTab.png]]

{| border="0"
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|This opens the Visualization panel and displays the ''Path to Root'' which contains the concept and all parent concepts, up to and including the root concept.

You can also display the ''Term Neighbourhood'' which contains the immediate parent and children of the current concept, or the ''Mappings Neighbourhood'' which contains the mappings for the current concept. To do this, click the drop-down arrow at the top of the Visualization panel, and select '''term neighbourhood''' or '''mappings neighbourhood'''.

From here, you can drag concepts around the screen to optimize viewing. You can also display mappings, other concepts, and adjust the style of visualization used.
| [[Image:BioMixerEmbedDropDownArrow.png]]
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<h2>Displaying related concepts and mappings</h2>

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|Once you have visualized a concept, you can expand the visualization to include the child concepts or mappings from any item. To do this, click the arrow below the desired concept or mapping, and then select:
* '''Concepts''': This will display the children of the concept, if applicable.
* '''Mappings''': This will display any mappings related to the concept, if applicable.
| [[Image:BioMixerEmbedDisplayChildConcepts.png|right]]
|}

[[Image:BioMixerEmbedChildConceptsDisplayed.png]]

You can expand the concepts and mappings outside of the current ontology. This makes it possible to visualize multiple ontologies at once and see the relationships between them. To make it easier to see relationships, BioPortal uses colors to identify ontologies. However, depending on how many ontologies you are working with, some colors may be duplicated. For information, see the section on [[#Nodes|Nodes]].

<h2>Viewing information about a concept or mapping</h2>
You can hover over a concept or mapping to display the name and ID of the ontology the item resides in.

[[Image:BioMixerEmbedCircleLayout.png]]

<h2>Removing a mapping or concept from a visualization</h2>
If a mapping or concept is no longer of interest to you, you can remove the related ontology from the visualization. You cannot remove a concept or mapping without removing its entire ontology. For information, see the section on [[#Nodes|Nodes]].

<h2>Changing how concepts and mappings are displayed</h2>
When visualizing ontology information, you can adjust how the concepts and mappings are displayed. To do this, click the chevron in the top-right corner of the Visualization panel.

[[Image:BioMixerEmbedOpenStackedPanel.png]]

This displays a panel with three groups of options: Nodes, Arcs, and Layouts.

<h3>Nodes</h3>
The Nodes portion of the side panel displays a list of the ontologies that are currently visualized, either through mappings or expanded concepts. It also displays the color associated with an ontology.

You can choose to remove a particular ontology from the visualization. To do this, clear the check box next to the ontology name.

You can also choose to not use colors to identify ontologies. To do this, clear the '''Color Concept Nodes by Ontology''' check box.

<h3>Arcs</h3>
By default, concepts are connected by a solid line with arrows that point towards the parent concept. Mappings are connected by a dashed line. If desired, you can change the color and style of these connections using the Arcs portion of the side panel.

The Arcs options are divided into separate controls for the concept relationships and the concept mappings. You can change the following options:
* '''Arcs Visible''': This check box controls whether lines are displayed.
* '''Arc Color''': This box defines the color of the lines that connect concepts or mappings. You can use any seven-character HTML color code.
* '''Arc Style''': This drop-down list defines the style of the line displayed (solid or dashed).
* '''Arc Thickness''': This drop-down list defines the thickness of the line displayed, in pixels.

Once you are finished, click the '''Update Arcs''' button and the changes will be applied to your visualization. Please note that there are two Update Arcs buttons – one for the options that control concept relationships, and one for the options that control concept mappings.

[[Image:BioMixerEmbedArcsOptions.png]]

<h3>Layouts</h3>
You can adjust the style of visualization used to optimize the display and to make it easier to view related information. The Layouts portion of the side panel displays four different layouts:
* '''Circle Layout''': This layout displays the concepts and mappings in a circle.
* '''Vertical Layout''': This layout displays the concepts and mappings with child/parent relationships organized vertically.
* '''Horizontal Layout''': This layout displays the concepts and mappings with child/parent relationships organized horizontally.
* '''Force-Directed Layout''': This layout positions the concepts and mappings so that all the edges are of more or less equal length and with as few crossing edges as possible. Use the Force-Directed Layout when working with clusters of data to optimize the display of related groups of information.

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